Please install R library:
library(CMF)
library(pROC)
library(data.table)
library(igraph)
library(sna)
Command to run gr-gCMF:
Rscript gr_gCMF.R matrix_list_gb.txt data/ outputFolder/
matrix_list_gb.txt file contains:
1st column: name list of input matrices.
2nd column: binary value {1,0} whether the input martrix file required graph featuers extraction.
3rd column: entity type(index number) corresponds to the row in the matrix (entity type row index).
4th column: entity type(index number) corresponds to the column in the matrix (entity type column index).
data/ folder contains a list of files listed in the first argument
outputFolder/ is your output folder ended with slash /
All columns are separated by tab delimited.
If you find this useful for your research, we would be appreciated if you cite the following papers:
@article{liany2020predicting,
title={Predicting synthetic lethal interactions using heterogeneous data sources},
author={Liany, Herty and Jeyasekharan, Anand and Rajan, Vaibhav},
journal={Bioinformatics},
volume={36},
number={7},
pages={2209--2216},
year={2020},
publisher={Oxford University Press}
}